This article presents the results of the research undertaken at the Faculty of Management and Economics, Tomas Bata University in Zlin. The research focuses on the efficiency of the healthcare system. One of the goals was to compare the efficiency of private horizontally integrated hospitals and horizontally integrated hospitals owned by county, town or municipality. To evaluate the efficiency the Data Envelopment Analysis method was used, which is a benchmarking method applied to measure the efficiency of homogeneous organisational units. When undertaking such measuring it is crucial to assume that inputs are minimalised and outputs are maximised, i.e. outputs must bring a positive result while inputs must be as low as possible. Even though the research did not prove that either private horizontally integrated hospitals or horizontally integrated hospitals owned by the county, town or municipality to be more efficient than the others, the results are valuable as they point at specific options for increasing the efficiency of individual hospitals.